data_452D # _model_server_result.job_id ViIRJEou8IevZNgeDfw4xg _model_server_result.datetime_utc '2024-10-18 15:31:31' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 452d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":3016}' # _entry.id 452D # _exptl.entry_id 452D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 452D _cell.length_a 30.161 _cell.length_b 30.161 _cell.length_c 39.692 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 452D _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 30.161 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1001 1_555 A N1 DG 6 A DG 1006 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1001 1_555 A O6 DG 6 A DG 1006 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1001 1_555 A N2 DG 6 A DG 1006 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 1002 1_555 A N3 DC 5 A DC 1005 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 1002 1_555 A O2 DC 5 A DC 1005 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 1002 1_555 A N4 DC 5 A DC 1005 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DT 3 A DT 1003 1_555 A N1 DA 4 A DA 1004 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 DT 3 A DT 1003 1_555 A N6 DA 4 A DA 1004 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 DA 4 A DA 1004 1_555 A N3 DT 3 A DT 1003 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N6 DA 4 A DA 1004 1_555 A O4 DT 3 A DT 1003 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 5 A DC 1005 1_555 A N1 DG 2 A DG 1002 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 5 A DC 1005 1_555 A O6 DG 2 A DG 1002 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 5 A DC 1005 1_555 A N2 DG 2 A DG 1002 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DG 6 A DG 1006 1_555 A N3 DC 1 A DC 1001 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 DG 6 A DG 1006 1_555 A O2 DC 1 A DC 1001 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 DG 6 A DG 1006 1_555 A N4 DC 1 A DC 1001 4_655 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 MPD sing 197 n n C1 H11 MPD sing 198 n n C1 H12 MPD sing 199 n n C1 H13 MPD sing 200 n n C2 O2 MPD sing 201 n n C2 CM MPD sing 202 n n C2 C3 MPD sing 203 n n O2 HO2 MPD sing 204 n n CM HM1 MPD sing 205 n n CM HM2 MPD sing 206 n n CM HM3 MPD sing 207 n n C3 C4 MPD sing 208 n n C3 H31 MPD sing 209 n n C3 H32 MPD sing 210 n n C4 O4 MPD sing 211 n n C4 C5 MPD sing 212 n n C4 H4 MPD sing 213 n n O4 HO4 MPD sing 214 n n C5 H51 MPD sing 215 n n C5 H52 MPD sing 216 n n C5 H53 MPD sing 217 n n # _atom_sites.entry_id 452D _atom_sites.fract_transf_matrix[1][1] 0.033155 _atom_sites.fract_transf_matrix[1][2] 0.019142 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.038285 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.025194 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 9AD A 1 3013 3013 9AD 9AD . C 2 9AD A 1 3015 3015 9AD 9AD . D 3 MPD A 1 3016 3016 MPD MPD . E 4 HOH A 1 4001 4001 HOH HOH . E 4 HOH A 2 4002 4002 HOH HOH . E 4 HOH A 3 4003 4003 HOH HOH . E 4 HOH A 4 4004 4004 HOH HOH . E 4 HOH A 5 4005 4005 HOH HOH . E 4 HOH A 6 4006 4006 HOH HOH . E 4 HOH A 7 4007 4007 HOH HOH . E 4 HOH A 8 4008 4008 HOH HOH . E 4 HOH A 9 4009 4009 HOH HOH . E 4 HOH A 10 4010 4010 HOH HOH . E 4 HOH A 11 4011 4011 HOH HOH . E 4 HOH A 12 4012 4012 HOH HOH . E 4 HOH A 13 4013 4013 HOH HOH . E 4 HOH A 14 4014 4014 HOH HOH . E 4 HOH A 15 4015 4015 HOH HOH . E 4 HOH A 16 4016 4016 HOH HOH . E 4 HOH A 17 4017 4017 HOH HOH . E 4 HOH A 18 4018 4018 HOH HOH . E 4 HOH A 19 4019 4019 HOH HOH . E 4 HOH A 20 4020 4020 HOH HOH . E 4 HOH A 21 4021 4021 HOH HOH . E 4 HOH A 22 4022 4022 HOH HOH . E 4 HOH A 23 4023 4023 HOH HOH . E 4 HOH A 24 4024 4024 HOH HOH . E 4 HOH A 25 4025 4025 HOH HOH . E 4 HOH A 26 4026 4026 HOH HOH . E 4 HOH A 27 4027 4027 HOH HOH . E 4 HOH A 28 4028 4028 HOH HOH . E 4 HOH A 29 4029 4029 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 MPD . . . D 3 7.617 -13.26 10.537 0.5 26.01 ? C1 MPD 3016 A 1 HETATM 2 C C2 MPD . . . D 3 8.016 -13.053 11.926 0.5 24.05 ? C2 MPD 3016 A 1 HETATM 3 O O2 MPD . . . D 3 9.132 -12.441 11.612 0.5 27.55 ? O2 MPD 3016 A 1 HETATM 4 C CM MPD . . . D 3 8.728 -14.22 12.501 0.5 31.3 ? CM MPD 3016 A 1 HETATM 5 C C3 MPD . . . D 3 7.054 -12.815 12.767 0.5 11.02 ? C3 MPD 3016 A 1 HETATM 6 C C4 MPD . . . D 3 5.927 -12.306 12.737 0.5 14.54 ? C4 MPD 3016 A 1 HETATM 7 O O4 MPD . . . D 3 5.026 -11.915 13.569 0.5 14.74 ? O4 MPD 3016 A 1 HETATM 8 H H11 MPD . . . D 3 8.394 -13.452 10.006 0.5 39.01 ? H11 MPD 3016 A 1 HETATM 9 H H12 MPD . . . D 3 7.191 -12.467 10.204 0.5 39.01 ? H12 MPD 3016 A 1 HETATM 10 H H13 MPD . . . D 3 7.005 -13.998 10.486 0.5 39.01 ? H13 MPD 3016 A 1 HETATM 11 H HM1 MPD . . . D 3 9.675 -14.077 12.444 0.5 46.94 ? HM1 MPD 3016 A 1 HETATM 12 H HM2 MPD . . . D 3 8.494 -15.011 12.01 0.5 46.94 ? HM2 MPD 3016 A 1 HETATM 13 H HM3 MPD . . . D 3 8.475 -14.328 13.421 0.5 46.94 ? HM3 MPD 3016 A 1 HETATM 14 H H31 MPD . . . D 3 6.885 -13.689 13.154 0.5 13.23 ? H31 MPD 3016 A 1 HETATM 15 H H32 MPD . . . D 3 7.498 -12.312 13.467 0.5 13.23 ? H32 MPD 3016 A 1 HETATM 16 H H4 MPD . . . D 3 5.435 -12.918 12.167 0.5 17.45 ? H4 MPD 3016 A 1 HETATM 17 H H42 MPD . . . D 3 6.068 -11.516 12.192 0.5 17.45 ? H42 MPD 3016 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #